cdm-dataportal / modules / cdm_dataportal / includes / occurrences.inc @ 4186a152
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<?php |
|---|---|
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/** |
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* @file |
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* Functions for dealing with CDM entities of type SpecimenOrOccurrences |
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* |
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* @copyright |
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* (C) 2007-2012 EDIT |
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* European Distributed Institute of Taxonomy |
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* http://www.e-taxonomy.eu |
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* |
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* The contents of this module are subject to the Mozilla |
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* Public License Version 1.1. |
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* @see http://www.mozilla.org/MPL/MPL-1.1.html |
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* |
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* @author |
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* - Andreas Kohlbecker <a.kohlbecker@BGBM.org> |
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*/ |
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|
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|
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/** |
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* Provides the HTML markup for a specimen page |
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* |
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* @param $specimen |
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* |
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* @return string |
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* The markup for a specimen page |
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*/ |
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function render_cdm_specimen_page($specimen) |
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{
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|
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$specimen_details = compose_cdm_specimen_or_observation($specimen, true); |
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//$detail_html .= drupal_render($specimen_details); |
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|
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$specimen->_fieldObjectMedia = cdm_ws_get(CDM_WS_DERIVEDUNIT_FACADE, array( |
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$specimen->uuid, |
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'fieldObjectMediaDTO', |
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)); |
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$specimen->_derivedUnitMedia = cdm_ws_get(CDM_WS_DERIVEDUNIT_FACADE, array( |
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$specimen->uuid, |
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'derivedUnitMedia', |
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)); |
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$gallery_settings = getGallerySettings(CDM_DATAPORTAL_SPECIMEN_GALLERY_NAME); |
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$captionElements = array( |
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'#uri' => t('open media'),
|
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); |
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if (isset($specimen->fieldObjectMediaDTO) ) {
|
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$gallery_html = compose_cdm_media_gallerie(array( |
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'mediaList' => $specimen->fieldObjectMediaDTO, |
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'galleryName' => $specimen->titleCache, |
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'maxExtend' => $gallery_settings['cdm_dataportal_media_maxextend'], |
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'cols' => $gallery_settings['cdm_dataportal_media_cols'], |
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'maxRows' => isset($gallery_settings['cdm_dataportal_media_maxRows']) ? isset($gallery_settings['cdm_dataportal_media_maxRows']) : null, |
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'captionElements' => $captionElements, |
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'mediaLinkType' => 'LIGHTBOX', |
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'alternativeMediaUri' => NULL, |
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'galleryLinkUri' => NULL, |
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)); |
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$specimen_details[] = markup_to_render_array($gallery_html); |
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} |
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|
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if (isset($specimen->_derivedUnitMedia) ) {
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$gallery_html = compose_cdm_media_gallerie(array( |
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'mediaList' => $specimen->_derivedUnitMedia, |
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'galleryName' => $specimen->titleCache, |
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'maxExtend' => $gallery_settings['cdm_dataportal_media_maxextend'], |
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'cols' => $gallery_settings['cdm_dataportal_media_cols'], |
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'maxRows' => isset($gallery_settings['cdm_dataportal_media_maxRows']) ? isset($gallery_settings['cdm_dataportal_media_maxRows']) : null, |
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'captionElements' => $captionElements, |
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'mediaLinkType' => 'LIGHTBOX', |
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'alternativeMediaUri' => NULL, |
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'galleryLinkUri' => NULL, |
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)); |
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$specimen_details[] = markup_to_render_array($gallery_html); |
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} |
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|
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$specimen_array = $specimen_details; |
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$output = ""; |
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foreach($specimen_array as $value){
|
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$renderArray = array( |
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'#theme' => 'item_list', |
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'#items' => array($value), |
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'#type' => 'ul'); |
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$output .= drupal_render($renderArray); |
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} |
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|
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|
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return $output; |
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} |
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|
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|
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/** |
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* Provides the HTML markup for a specimen page |
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* |
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* @param $specimen |
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* |
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* @return string |
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* The markup for a specimen page |
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*/ |
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function render_cdm_specimenDTO_page($specimen, $is_specimen_page = false) |
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{
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$detail_html = ""; |
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//link to specimen page |
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$pathToSpecimen = path_to_specimen($specimen->uuid); |
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if (!$is_specimen_page) {
|
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$specimenPageLink = l($specimen->accessionNumber, $pathToSpecimen, array('attributes' => array('target' => '_blank')));
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$detail_html .= "<strong>Specimen summary: $specimenPageLink</strong><br>"; |
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} |
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|
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|
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if($is_specimen_page) {
|
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if($specimen->citation){
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$detail_html .= "<br>".$specimen->citation."<br>"; |
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|
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} |
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} |
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if ($specimen->preferredStableUri) {
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$stableIdentifierLink = l($specimen->preferredStableUri, $specimen->preferredStableUri, array('attributes' => array('target' => '_blank')));
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$detail_html .= create_label("Preferred stable URI") . $stableIdentifierLink . "<br>";
|
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} |
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if ($is_specimen_page) {
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// associated taxa |
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if ($specimen->associatedTaxa) {
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$detail_html .= "<br>"; |
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$detail_html .= create_label("Associated with");
|
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if (sizeof($specimen->associatedTaxa) > 1) {
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$detail_html .= "<br>"; |
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} |
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foreach ($specimen->associatedTaxa as $associatedTaxon) {
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$detail_html .= l($associatedTaxon->value, path_to_taxon($associatedTaxon->key, "specimens"));//$associatedTaxon->second."<br>"; |
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} |
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$detail_html .= "<br>"; |
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} |
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} |
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// - type information |
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$types = ""; |
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if (isset($specimen->types)) {
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//typed taxa |
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foreach ($specimen->types as $typeStatus => $typedTaxa) {
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if($specimen->types){
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if(empty($typeStatus) || $typeStatus == "_empty_"|| $typeStatus == ""){
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$detail_html .= "<i>Type for:</i> "; |
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} else {
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$detail_html .= "<i>".$typeStatus."</i> of "; |
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} |
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foreach($typedTaxa as $typedTaxon){
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$detail_html .= $typedTaxon." "; |
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|
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} |
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} else {
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$types .= $typeStatus . " "; |
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|
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} |
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} |
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} |
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$derivateDataDTO = $specimen->derivateDataDTO; |
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// - specimen scans |
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$specimenScans = create_html_links($derivateDataDTO->specimenScans, true); |
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// - molecular data |
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$molecularData = ""; |
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if ($derivateDataDTO->molecularDataList) {
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foreach ($derivateDataDTO->molecularDataList as $molecular) {
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//provider link |
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if (isset($molecular->providerLink)) {
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$molecularData .= create_html_link($molecular->providerLink, true); |
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} else {
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$molecularData .= "[no provider]"; |
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} |
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//contig link |
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if (isset($molecular->contigFiles)) {
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$molecularData .= "["; |
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if (sizeof($molecular->contigFiles) > 0) {
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foreach ($molecular->contigFiles as $contigFile) {
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if (isset($contigFile->contigLink)) {
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if (isset($contigFile->contigLink->uri) and $contigFile->contigLink->uri != null) {
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$molecularData .= create_html_link($contigFile->contigLink, true) . " "; |
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} |
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} else {
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$molecularData .= "no contig "; |
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} |
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//primer links |
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if (isset($contigFile->primerLinks)) {
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$molecularData .= create_html_links($contigFile->primerLinks, true); |
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} |
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} |
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} |
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$molecularData = rtrim($molecularData, " "); |
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$molecularData .= "]"; |
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} |
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//FIXME separate with comma (remove trailing comma) |
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} |
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} |
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// - detail images |
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$detailImages = create_html_links($derivateDataDTO->detailImages, true); |
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|
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if ($types) {
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$detail_html .= $is_specimen_page ? "<br>" : ""; |
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$detail_html .= create_label("Type(s)") . $types . "<br>";
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} |
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if ($specimenScans and !$is_specimen_page) {
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$detail_html .= create_label("Specimen Scans") . $specimenScans . "<br>";
|
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} |
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//specimen scan image gallery |
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if ($is_specimen_page and isset($derivateDataDTO->specimenScanUuids) and !empty($derivateDataDTO->specimenScanUuids)) {
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$detail_html .= addImageGallery("Specimen scans", $derivateDataDTO->specimenScanUuids);
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} |
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|
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if ($molecularData) {
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$detail_html .= $is_specimen_page ? "<br>" : ""; |
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$detail_html .= create_label("Molecular Data") . $molecularData . "<br>";
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} |
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|
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if ($detailImages and !$is_specimen_page) {
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$detail_html .= create_label("Detail Images") . $detailImages . "<br>";
|
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} |
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|
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//detail image gallery |
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if ($is_specimen_page and isset($derivateDataDTO->detailImageUuids) and !empty($derivateDataDTO->detailImageUuids)) {
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$detail_html .= addImageGallery("Detail Images", $derivateDataDTO->detailImageUuids);
|
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} |
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|
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//character data |
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if ($specimen->characterData) {
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$detail_html .= $is_specimen_page ? "<br>" : ""; |
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$detail_html .= create_label("Character Data");
|
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if ($is_specimen_page) {
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$detail_html .= "<br>"; |
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foreach ($specimen->characterData as $characterStatePair) {
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$detail_html .= "<i>" . $characterStatePair->first . "</i>:" . $characterStatePair->second; |
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$detail_html .= "<br>"; |
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} |
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} else {
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$detail_html .= l("detail page", $pathToSpecimen, array('attributes' => array('target' => '_blank')));
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$detail_html .= "<br>"; |
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} |
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} |
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return $detail_html; |
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} |
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|
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function addImageGallery($galleryName, $imageUuids) |
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{
|
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$images = array(); |
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foreach ($imageUuids as $uuid) {
|
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$images[] = cdm_ws_get(CDM_WS_PORTAL_MEDIA, $uuid); |
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} |
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|
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$gallery_html = ''; |
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if (count($imageUuids) > 0) {
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$gallery_settings = getGallerySettings(CDM_DATAPORTAL_SPECIMEN_GALLERY_NAME); |
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$captionElements = array( |
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'title', |
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'rights', |
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); |
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$alternativeMediaUris = array(); |
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foreach ($images as $image) {
|
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$mediaUri = getMediaUri($image); |
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if ($mediaUri) {
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$alternativeMediaUris[] = $mediaUri; |
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} else {
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$alternativeMediaUris[] = path_to_media($image->uuid); |
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} |
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} |
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|
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$gallery_html = compose_cdm_media_gallerie(array( |
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'mediaList' => $images, |
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'galleryName' => $galleryName, |
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'maxExtend' => $gallery_settings['cdm_dataportal_media_maxextend'], |
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'cols' => $gallery_settings['cdm_dataportal_media_cols'], |
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'maxRows' => isset($gallery_settings['cdm_dataportal_media_maxRows']) ? isset($gallery_settings['cdm_dataportal_media_maxRows']) : null, |
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'captionElements' => $captionElements, |
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'mediaLinkType' => 'LIGHTBOX', |
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'alternativeMediaUri' => $alternativeMediaUris, |
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'galleryLinkUri' => NULL, |
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)); |
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} |
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return "<br>" . create_label($galleryName) . "<br>" . $gallery_html; |
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} |
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|
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function getMediaUri($media) |
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{
|
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if (isset($media->representations) && sizeof($media->representations) == 1 |
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&& isset($media->representations[0]->parts) && |
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sizeof($media->representations[0]->parts) == 1) {
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return $media->representations[0]->parts[0]->uri; |
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} |
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return null; |
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} |
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|
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|
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/** |
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* Formats the given string to a label for displaying key-object pairs in HTML |
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* @return string |
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*/ |
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function create_label($label) |
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{
|
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return "<span class='specimen_table_label'>" . $label . ": </span>"; |
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} |
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|
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/** |
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* Compose an render array from a CDM DerivedUnitFacade object. |
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* |
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* compose_hook() implementation |
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* |
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* @param object $specimenOrObservation |
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* the CDM instance of type SpecimenOrObservation to compose |
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* the render array for |
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* @param array $derivatives |
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* the render array which contains the compositions of the derivatives |
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* of the supplied $specimenOrObservation |
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* |
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* @return array |
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* the supplied render array $derivatives to which the composition of the supplied |
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* $specimenOrObservation has been added to |
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* |
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* @ingroup compose |
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*/ |
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|
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function compose_cdm_specimen_or_observation($specimen_or_observation, $isSpecimen_page = false, &$derivatives = null) |
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{
|
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$exclude_occurrence_fields = &drupal_static(__FUNCTION__); |
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if (!isset($exclude_occurrence_fields)) {
|
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$exclude_occurrence_fields = array( |
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|
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'titleCache', |
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'protectedTitleCache', |
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'derivedUnitMedia', |
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'created', |
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'publish', |
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'updated', |
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'class', |
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'uuid', |
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'' |
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); |
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} |
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if (variable_get('cdm_dataportal_compressed_specimen_derivate_table') || !$isSpecimen_page){
|
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$exclude_occurrence_fields[] = 'derivationEvents'; |
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} |
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|
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|
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// only show uuid it the user is logged in |
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// if(user_is_logged_in() && ($a_idx = array_search('uuid', $exclude_occurrence_fields)) !== FALSE ) {
|
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// unset($exclude_occurrence_fields[$a_idx]); |
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// } |
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|
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if (!isset($derivatives)) {
|
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$derivatives = array(); |
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} |
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|
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$descriptions = null; |
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$derivedFrom = null; |
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|
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|
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|
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if (is_object($specimen_or_observation)) {
|
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|
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// request again for deeper initialization |
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$specimen_or_observation = cdm_ws_get("portal/" . CDM_WS_OCCURRENCE, $specimen_or_observation->uuid);
|
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if ($specimen_or_observation->class == 'FieldUnit'){
|
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$specimen_or_observation->_derivedUnitMedia = cdm_ws_get(CDM_WS_DERIVEDUNIT_FACADE, array( |
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$specimen_or_observation->uuid, |
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'fieldObjectMediaDTO', |
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)); |
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}else{
|
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$specimen_or_observation->_derivedUnitMedia = cdm_ws_get(CDM_WS_DERIVEDUNIT_FACADE, array( |
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$specimen_or_observation->uuid, |
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'derivedUnitMedia', |
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)); |
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} |
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|
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$type_label = $specimen_or_observation->class; |
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RenderHints::setFootnoteListKey($type_label . '-' . $specimen_or_observation->uuid); |
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|
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// collect typeStatus as label |
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if (isset($specimen_or_observation->specimenTypeDesignations)) {
|
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$type_status = array(); |
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foreach ($specimen_or_observation->specimenTypeDesignations as $typeDesignation) {
|
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if (isset($typeDesignation->typeStatus->representation_L10n)) {
|
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$type_status[] = $typeDesignation->typeStatus->representation_L10n; |
| 378 |
} |
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} |
| 380 |
if (count($type_status) > 0) {
|
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$type_label = implode(', ', $type_status);
|
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} |
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} |
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|
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$title = $type_label . ': ' . $specimen_or_observation->titleCache; |
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|
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$groups = array(); |
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|
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// --- add initialized fields |
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foreach (get_object_vars($specimen_or_observation) as $field => $value) {
|
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if (!in_array($field, $exclude_occurrence_fields) && ($value && (!is_object($value) || isset($value->class)))) {
|
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switch ($field) {
|
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|
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/* ---- java.lang.Object --- */ |
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case 'class': |
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if ($value != '' /* FieldUnit' */) {
|
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@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value); |
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} |
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break; |
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|
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case 'markers': |
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$dd_elements = array(); |
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foreach ($value as $marker) {
|
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$dd_elements[] = compose_cdm_marker($marker); |
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} |
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@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements); |
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break; |
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|
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|
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case 'annotations': |
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$dd_elements = array(); |
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foreach ($value as $annotation) {
|
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// TODO respect annotation type filter settings |
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$dd_elements[] = $annotation->text; |
| 415 |
} |
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@_description_list_group_add($groups, t('Notes'), $dd_elements);
|
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break; |
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|
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/* ---- SpecimenOrObservationBase --- */ |
| 420 |
case 'sex': |
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case 'lifeStage': |
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case 'kindOfUnit': |
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@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value->representation_L10n); |
| 424 |
break; |
| 425 |
|
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case 'definition': |
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// TODO |
| 428 |
break; |
| 429 |
|
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case 'preferredStableUri': |
| 431 |
|
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@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), array(array('#markup' => cdm_external_uri($value, false))));
|
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break; |
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|
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case 'specimenTypeDesignations': |
| 436 |
|
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//TODO: better display of details!! |
| 438 |
@_description_list_group_add( |
| 439 |
$groups, |
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cdm_occurrence_field_name_label($field), |
| 441 |
array( |
| 442 |
'#markup' => theme('cdm_typedesignations', array('typeDesignations' => $value)),
|
| 443 |
) |
| 444 |
); |
| 445 |
break; |
| 446 |
|
| 447 |
case 'determinations': |
| 448 |
$dd_elements = array(); |
| 449 |
$glue = ', '; |
| 450 |
|
| 451 |
foreach ($value as $determinationEvent) {
|
| 452 |
$timeperiod_string = NULL; |
| 453 |
if (isset($determinationEvent->timeperiod)) {
|
| 454 |
$timeperiod_string = timePeriodToString($determinationEvent->timeperiod); |
| 455 |
} |
| 456 |
$weight = isset($determinationEvent->preferred) && $determinationEvent->preferred == 1 ? '0' : ($timeperiod_string ? $timeperiod_string : '1'); |
| 457 |
// check key exists |
| 458 |
while (array_key_exists($weight, $dd_elements)) {
|
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$weight .= '0'; |
| 460 |
} |
| 461 |
|
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$taxon_name = ''; |
| 463 |
$name_link = ''; |
| 464 |
if ($determinationEvent->taxonName) {
|
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$taxon_name = $determinationEvent->taxonName; |
| 466 |
} else if ($determinationEvent->taxon) {
|
| 467 |
$taxon_name = cdm_ws_get(CDM_WS_TAXON . '/$0/name', $determinationEvent->taxon->uuid); |
| 468 |
$name_link = path_to_taxon($determinationEvent->taxon->uuid); |
| 469 |
} |
| 470 |
if ($taxon_name) {
|
| 471 |
$taxon_html = render_taxon_or_name($taxon_name, $name_link); |
| 472 |
$dd_elements[$weight] = $taxon_html; |
| 473 |
} |
| 474 |
if (isset($determinationEvent->modifier)) {
|
| 475 |
$dd_elements[$weight] .= cdm_term_representation($determinationEvent->modifier); |
| 476 |
} |
| 477 |
if ($timeperiod_string) {
|
| 478 |
$dd_elements[$weight] .= $glue . $timeperiod_string; |
| 479 |
} |
| 480 |
if (isset($determinationEvent->actor->titleCache)) {
|
| 481 |
$dd_elements[$weight] .= $glue . $determinationEvent->actor->titleCache; |
| 482 |
} |
| 483 |
if (isset($determinationEvent->description)) {
|
| 484 |
$dd_elements[$weight] .= $glue . $determinationEvent->description; |
| 485 |
} |
| 486 |
} |
| 487 |
ksort($dd_elements); |
| 488 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label('determinations'), $dd_elements);
|
| 489 |
break; |
| 490 |
|
| 491 |
case 'descriptions': |
| 492 |
$occurrence_featureTree = cdm_get_occurrence_featureTree(); |
| 493 |
$dd_elements = array(); |
| 494 |
|
| 495 |
foreach ($value as $description) {
|
| 496 |
$description = cdm_ws_get(CDM_WS_PORTAL_DESCRIPTION, $description->uuid); |
| 497 |
|
| 498 |
if($description->imageGallery == TRUE) {
|
| 499 |
continue; |
| 500 |
} |
| 501 |
$elements_by_feature = _mergeFeatureTreeDescriptions($occurrence_featureTree->root->childNodes, $description->elements); |
| 502 |
$description_render_elements = _block_get_renderable_array(make_feature_block_list($elements_by_feature, null)); |
| 503 |
$dd_elements[] = $description_render_elements; |
| 504 |
} |
| 505 |
|
| 506 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements); |
| 507 |
break; |
| 508 |
case '_derivedUnitMedia': |
| 509 |
if ($isSpecimen_page){
|
| 510 |
$gallery_settings = getGallerySettings(CDM_DATAPORTAL_SPECIMEN_GALLERY_NAME); |
| 511 |
$captionElements = array( |
| 512 |
'#uri' => t('open media'),
|
| 513 |
); |
| 514 |
$gallery_html = compose_cdm_media_gallerie(array( |
| 515 |
'mediaList' => $value, |
| 516 |
'galleryName' => $specimen_or_observation->titleCache, |
| 517 |
'maxExtend' => $gallery_settings['cdm_dataportal_media_maxextend'], |
| 518 |
'cols' => $gallery_settings['cdm_dataportal_media_cols'], |
| 519 |
'maxRows' => isset($gallery_settings['cdm_dataportal_media_maxRows']) ? isset($gallery_settings['cdm_dataportal_media_maxRows']) : null, |
| 520 |
'captionElements' => $captionElements, |
| 521 |
'mediaLinkType' => 'LIGHTBOX', |
| 522 |
'alternativeMediaUri' => NULL, |
| 523 |
'galleryLinkUri' => NULL, |
| 524 |
)); |
| 525 |
@_description_list_group_add($groups, "Detail Images:" , markup_to_render_array($gallery_html),'',20); |
| 526 |
} |
| 527 |
|
| 528 |
// $dd_elements[] = markup_to_render_array($gallery_html); |
| 529 |
|
| 530 |
break; |
| 531 |
case 'sources': |
| 532 |
$annotations_and_sources = handle_annotations_and_sources( |
| 533 |
$specimen_or_observation, |
| 534 |
array( |
| 535 |
'sources_as_content' => true, |
| 536 |
'link_to_name_used_in_source' => 1, |
| 537 |
'link_to_reference' => 0, |
| 538 |
'add_footnote_keys' => 0 |
| 539 |
), |
| 540 |
NULL, |
| 541 |
'' |
| 542 |
); |
| 543 |
if(!empty($annotations_and_sources['source_references'])){
|
| 544 |
@_description_list_group_add($groups, t('Sources') . ':', join(', ', $annotations_and_sources['source_references']),'',12 );
|
| 545 |
} |
| 546 |
break; |
| 547 |
|
| 548 |
|
| 549 |
/* ---- DerivedUnitBase --- */ |
| 550 |
case 'derivedFrom': |
| 551 |
$derivedFrom = $value; |
| 552 |
if ($isSpecimen_page) {
|
| 553 |
foreach ($derivedFrom->originals as $original) {
|
| 554 |
$pathToSpecimen = path_to_specimen($original->uuid); |
| 555 |
$description = ""; |
| 556 |
if (isset( $derivedFrom->description) && $derivedFrom->description != ''){
|
| 557 |
$description = $derivedFrom->description . ": "; |
| 558 |
} |
| 559 |
|
| 560 |
$originals[] = markup_to_render_array(l($description . $original->titleCache, $pathToSpecimen, array('attributes' => array('target' => '_blank'))));
|
| 561 |
if ($original->class == 'FieldUnit'){
|
| 562 |
$label = t('Field data');
|
| 563 |
}else{
|
| 564 |
$label = t('Derived from');
|
| 565 |
} |
| 566 |
@_description_list_group_add($groups, $label . ':', |
| 567 |
$originals, |
| 568 |
'', 13); |
| 569 |
} |
| 570 |
} |
| 571 |
break; |
| 572 |
case 'derivationEvents': |
| 573 |
$derivationEvents = $value; |
| 574 |
$derived_units = array(); |
| 575 |
if ($isSpecimen_page) {
|
| 576 |
foreach ($derivationEvents as $derivationEvent) {
|
| 577 |
foreach ($derivationEvent->derivatives as $derived_unit) {
|
| 578 |
$pathToSpecimen = path_to_specimen($derived_unit->uuid); |
| 579 |
$description = ""; |
| 580 |
if (isset($derived_unit->description) && $derived_unit->description != '') {
|
| 581 |
$description = $derived_unit->description . ": "; |
| 582 |
} |
| 583 |
|
| 584 |
$derived_units[] = markup_to_render_array(l($description . $derived_unit->titleCache, $pathToSpecimen, array('attributes' => array('target' => '_blank'))));
|
| 585 |
} |
| 586 |
} @_description_list_group_add($groups, t('Derivates') . ':',
|
| 587 |
$derived_units, |
| 588 |
'', 100); |
| 589 |
|
| 590 |
} |
| 591 |
break; |
| 592 |
|
| 593 |
case 'collection': |
| 594 |
$sub_dl_groups = array(); |
| 595 |
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('code'), $value->code, NULL, 1);
|
| 596 |
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('codeStandard'), $value->codeStandard, NULL, 2);
|
| 597 |
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('institute'), $value->institute, NULL, 3);
|
| 598 |
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('townOrLocation'), $value->townOrLocation, NULL, 4);
|
| 599 |
// TODO "superCollection" |
| 600 |
// TODO may have media |
| 601 |
|
| 602 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), |
| 603 |
array( |
| 604 |
array('#markup' => $value->titleCache),
|
| 605 |
array('#theme' => 'description_list', '#groups' => $sub_dl_groups)
|
| 606 |
) |
| 607 |
); |
| 608 |
break; |
| 609 |
|
| 610 |
case 'storedUnder': |
| 611 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label('storedUnder'), render_taxon_or_name($value));
|
| 612 |
break; |
| 613 |
|
| 614 |
|
| 615 |
/* ---- Specimen --- */ |
| 616 |
case 'sequences': |
| 617 |
$dd_elements = array(); |
| 618 |
foreach ($value as $sequence) {
|
| 619 |
$dd_elements[] = compose_cdm_sequence($sequence); |
| 620 |
} |
| 621 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements); |
| 622 |
break; |
| 623 |
|
| 624 |
// TODO preservation |
| 625 |
// TODO exsiccatum |
| 626 |
|
| 627 |
|
| 628 |
/* ---- FieldObservation --- */ |
| 629 |
case 'gatheringEvent': |
| 630 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label('collector'), $value->actor->titleCache, '', 1);
|
| 631 |
@_description_list_group_add($groups, t('Gathering date'), timePeriodToString($value->timeperiod), '', 2);
|
| 632 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label('description'), $value->description, '', 3);
|
| 633 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label('locality'), $value->locality->text, '', 10);
|
| 634 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label('country'), $value->country->representation_L10n, '', 4);
|
| 635 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label('collectingMethod'), $value->collectingMethod,'',5);
|
| 636 |
if (isset($value->absoluteElevation)) {
|
| 637 |
$min_max_markup = min_max_measure($value, 'absoluteElevation'); |
| 638 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label('absoluteElevation'), $min_max_markup, '',6);
|
| 639 |
} |
| 640 |
if (isset($value->distanceToGround)) {
|
| 641 |
$min_max_markup = min_max_measure($value, 'distanceToGround'); |
| 642 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label('distanceToGround'), $min_max_markup,'',7);
|
| 643 |
} |
| 644 |
if (isset($value->distanceToWaterSurface)) {
|
| 645 |
$min_max_markup = min_max_measure($value, 'distanceToWaterSurface'); |
| 646 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label('distanceToWaterSurface'), $min_max_markup, '',8);
|
| 647 |
} |
| 648 |
if (isset($value->collectingAreas) && count($value->collectingAreas) > 0) {
|
| 649 |
$area_representations = array(); |
| 650 |
foreach ($value->collectingAreas as $area) {
|
| 651 |
$area_representations[] = l($area->representation_L10n, path_to_named_area($area->uuid)); |
| 652 |
} |
| 653 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label('collectingAreas'),
|
| 654 |
array( |
| 655 |
array('#markup' => implode(', ', $area_representations))
|
| 656 |
),'',9 |
| 657 |
); |
| 658 |
} |
| 659 |
if (isset($value->exactLocation) && $value->exactLocation->sexagesimalString) {
|
| 660 |
$sub_dl_groups = array(); |
| 661 |
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('errorRadius'), $value->exactLocation->errorRadius, ' m', 1);
|
| 662 |
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('longitude'), round($value->exactLocation->longitude, 7), '°', 2);
|
| 663 |
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('latitude'), round($value->exactLocation->latitude, 7), '°', 3);
|
| 664 |
if (isset($value->exactLocation->referenceSystem)) {
|
| 665 |
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('referenceSystem'), $value->exactLocation->referenceSystem->representation_L10n, '', 4);
|
| 666 |
} |
| 667 |
|
| 668 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label('exactLocation'),
|
| 669 |
array( |
| 670 |
array('#markup' => $value->exactLocation->sexagesimalString),
|
| 671 |
array( |
| 672 |
'#theme' => 'description_list', |
| 673 |
'#groups' => $sub_dl_groups |
| 674 |
), |
| 675 |
),'',11 |
| 676 |
); |
| 677 |
} |
| 678 |
break; |
| 679 |
|
| 680 |
default: |
| 681 |
if (is_object($value) || is_array($value)) {
|
| 682 |
drupal_set_message("Unhandled type in compose_cdm_specimen_or_observation() for field " . $field, "warning");
|
| 683 |
} else {
|
| 684 |
_description_list_group_add($groups, cdm_occurrence_field_name_label($field), cdm_occurrence_field_name_label($value)); |
| 685 |
} |
| 686 |
|
| 687 |
} |
| 688 |
|
| 689 |
} |
| 690 |
} // END of loop over $derivedUnitFacade fields |
| 691 |
|
| 692 |
// Extensions |
| 693 |
$extensions = cdm_ws_fetch_all(CDM_WS_PORTAL_OCCURRENCE . '/' . $specimen_or_observation->uuid . '/extensions', array($specimen_or_observation->uuid)); |
| 694 |
if ($extensions && count($extensions)) {
|
| 695 |
|
| 696 |
$extensions_render_array = compose_extensions($extensions); |
| 697 |
@_description_list_group_add($groups, t('Extensions') . ':',
|
| 698 |
$extensions_render_array, |
| 699 |
'', 100); |
| 700 |
} |
| 701 |
|
| 702 |
|
| 703 |
|
| 704 |
// template_preprocess_description_list() is not worting by weight so we do it right here |
| 705 |
uasort($groups, 'element_sort'); |
| 706 |
|
| 707 |
$occurrence_elements = array( |
| 708 |
// '#title' => $title, |
| 709 |
'#theme' => 'description_list', |
| 710 |
'#groups' => $groups, |
| 711 |
'#attributes' => array('class' => html_class_attribute_ref($specimen_or_observation)),
|
| 712 |
); |
| 713 |
|
| 714 |
$derivatives[] = drupal_render($occurrence_elements); |
| 715 |
// all footnotes which has been assembled so far (e.g. from typeDesignations) to here |
| 716 |
// $foonote_li_elements = theme('cdm_footnotes', array('footnoteListKey' => RenderHints::getFootnoteListKey(), 'enclosingTag' => 'span'));
|
| 717 |
// if (!empty($foonote_li_elements)) {
|
| 718 |
// $derivatives[] = array( |
| 719 |
// '#markup' => '<div class="footnotes">' . $foonote_li_elements . '</div>', |
| 720 |
// ); |
| 721 |
// } |
| 722 |
|
| 723 |
// --- recurse into originals |
| 724 |
if (!isset($derivedFrom) && !$isSpecimen_page) {
|
| 725 |
$derivedFrom = cdm_ws_get( |
| 726 |
CDM_WS_OCCURRENCE, |
| 727 |
array($specimen_or_observation->uuid, 'derivedFrom') |
| 728 |
); |
| 729 |
} |
| 730 |
if (isset($derivedFrom) && !$isSpecimen_page) {
|
| 731 |
if (isset($derivedFrom->originals)) {
|
| 732 |
$derived_from_label = t('derived');
|
| 733 |
$preposition = t('from');
|
| 734 |
if(isset($derivedFrom->type)){
|
| 735 |
$derived_from_label = $derivedFrom->type->representation_L10n; |
| 736 |
if($derivedFrom->type->uuid == UUID_DERIVATIONEVENTTYPE_ACCESSIONING){
|
| 737 |
$preposition = t('of');
|
| 738 |
} |
| 739 |
} |
| 740 |
if (count($groups) > 0) {
|
| 741 |
// TODO annotations |
| 742 |
|
| 743 |
// only display the derived from information when the derivative has any element which will be diplayed |
| 744 |
$derivatives[] = array( |
| 745 |
'#markup' => '<div class="derived_from">' . $derived_from_label . ' ' . $preposition . ': </div>', |
| 746 |
); |
| 747 |
} |
| 748 |
foreach ($derivedFrom->originals as $original) {
|
| 749 |
compose_cdm_specimen_or_observation($original, $isSpecimen_page, $derivatives); |
| 750 |
} |
| 751 |
} |
| 752 |
} |
| 753 |
|
| 754 |
|
| 755 |
|
| 756 |
|
| 757 |
} // END of $specimenOrObservation exists |
| 758 |
|
| 759 |
return $derivatives; |
| 760 |
} |
| 761 |
|
| 762 |
|
| 763 |
/** |
| 764 |
* Compose an render array from a CDM Sequence object. |
| 765 |
* |
| 766 |
* compose_hook() implementation |
| 767 |
* |
| 768 |
* @param object $sequence |
| 769 |
* CDM instance of type Sequence |
| 770 |
* @return array |
| 771 |
* A render array containing the fields of the supplied $sequence |
| 772 |
* |
| 773 |
* @ingroup compose |
| 774 |
*/ |
| 775 |
function compose_cdm_sequence($sequence, $isSpecimenPage = false) |
| 776 |
{
|
| 777 |
|
| 778 |
$exclude_sequence_fields = &drupal_static(__FUNCTION__); |
| 779 |
if (!isset($exclude_sequence_fields)) {
|
| 780 |
$exclude_sequence_fields = array( |
| 781 |
'titleCache', |
| 782 |
'protectedTitleCache', |
| 783 |
'microReference', |
| 784 |
'created', |
| 785 |
'updated', |
| 786 |
'class', |
| 787 |
); |
| 788 |
} |
| 789 |
|
| 790 |
$groups = array(); |
| 791 |
|
| 792 |
// -- retrieve additional data if neesscary |
| 793 |
// TODO below call disabled since sequences are not yet supported, |
| 794 |
// see #3347 (services and REST service controller for molecular classes implemented) |
| 795 |
// |
| 796 |
// cdm_load_annotations($sequence); |
| 797 |
|
| 798 |
foreach (get_object_vars($sequence) as $field => $value) {
|
| 799 |
|
| 800 |
|
| 801 |
if (!in_array($field, $exclude_sequence_fields) && ($value && (!is_object($value) || isset($value->class)))) {
|
| 802 |
switch ($field) {
|
| 803 |
|
| 804 |
case 'geneticAccessionNumber'; |
| 805 |
|
| 806 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value, NULL, 2); |
| 807 |
break; |
| 808 |
|
| 809 |
|
| 810 |
case 'dnaMarker': // FIXME 3.3 now dnaMarker (DefinedTerm) if multiple amplifications where used to build this consensus sequence it may be the super set of the markers used in amplification. |
| 811 |
if (isset($value->name)) {
|
| 812 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value->name, NULL, 3); |
| 813 |
} |
| 814 |
if (isset($value->description)) {
|
| 815 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field) . ' ' . t('description'), $value->description, NULL, 4);
|
| 816 |
} |
| 817 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field) , $value, NULL, 4); |
| 818 |
break; |
| 819 |
|
| 820 |
case 'consensusSequence': |
| 821 |
// format in genbank style, force linebreaks after each 70 nucleotites |
| 822 |
// see also http://stackoverflow.com/questions/499137/css-how-can-i-force-a-long-string-without-any-blank-to-be-wrapped-in-xul-and |
| 823 |
if ($value->length > 0) {
|
| 824 |
@_description_list_group_add( |
| 825 |
$groups, |
| 826 |
cdm_occurrence_field_name_label($field), |
| 827 |
array( |
| 828 |
array( |
| 829 |
'#markup' => '<div class="sequence-length">' . $value->length . ' ' . t('pb') . '</div><div>' . wordwrap($value->string, 70, '</br>', TRUE) . '</div>',
|
| 830 |
'#wrapper_attributes' => array('class' => 'dna-sequence')
|
| 831 |
) |
| 832 |
), |
| 833 |
5); |
| 834 |
} |
| 835 |
break; |
| 836 |
|
| 837 |
case 'dnaSample': // FIXME 3.3 implement |
| 838 |
break; |
| 839 |
case 'singleReads': // FIXME 3.3 implement |
| 840 |
break; |
| 841 |
case 'contigFile': // FIXME 3.3 implement - Media |
| 842 |
break; |
| 843 |
case 'pherograms': // FIXME 3.3 implement - Media |
| 844 |
break; |
| 845 |
case 'haplotype': // FIXME 3.3 implement |
| 846 |
break; |
| 847 |
case 'dateSequenced': // FIXME 3.3 now in SingelRead |
| 848 |
@_description_list_group_add($groups, t('Sequencing date'), timePeriodToString($value), NULL, 6);
|
| 849 |
break; |
| 850 |
|
| 851 |
case 'barcode': // boolean |
| 852 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value ? 'Yes' : 'No', NULL, 7); |
| 853 |
break; |
| 854 |
case 'barcodeSequencePart': // FIXME 3.3 implement, compose sequence |
| 855 |
break; |
| 856 |
|
| 857 |
case 'citation': |
| 858 |
@_description_list_group_add($groups, |
| 859 |
cdm_occurrence_field_name_label($field), |
| 860 |
theme('cdm_reference', array('reference' => $value, 'microReference' => $sequence->microReference)),
|
| 861 |
NULL, |
| 862 |
8 |
| 863 |
); |
| 864 |
break; |
| 865 |
|
| 866 |
case 'publishedIn': |
| 867 |
@_description_list_group_add($groups, |
| 868 |
cdm_occurrence_field_name_label($field), |
| 869 |
theme('cdm_reference', array('reference' => $value)),
|
| 870 |
NULL, |
| 871 |
7 |
| 872 |
); |
| 873 |
break; |
| 874 |
|
| 875 |
case 'rights': |
| 876 |
array_merge($groups, cdm_rights_as_dl_groups($value)); |
| 877 |
break; |
| 878 |
|
| 879 |
case 'annotations': |
| 880 |
$dd_elements = array(); |
| 881 |
foreach ($value as $annotation) {
|
| 882 |
// TODO respect annotation type filter settings |
| 883 |
$dd_elements[] = $annotation->text; |
| 884 |
} |
| 885 |
@_description_list_group_add($groups, t('Notes'), $dd_elements, NULL, 9);
|
| 886 |
break; |
| 887 |
|
| 888 |
case 'markers': |
| 889 |
$dd_elements = array(); |
| 890 |
foreach ($value as $marker) {
|
| 891 |
$dd_elements[] = compose_cdm_marker($marker); |
| 892 |
} |
| 893 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements, NULL, 10); |
| 894 |
break; |
| 895 |
|
| 896 |
case 'chromatograms': |
| 897 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), |
| 898 |
array( |
| 899 |
'#markup' => compose_cdm_media_gallerie(array('medialist' => $value)),
|
| 900 |
), |
| 901 |
NULL, |
| 902 |
11); |
| 903 |
break; |
| 904 |
|
| 905 |
default: |
| 906 |
if (is_object($value) || is_array($value)) {
|
| 907 |
drupal_set_message("Unhandled type in compose_cdm_sequence() for field " . $field, "warning");
|
| 908 |
} else {
|
| 909 |
if (!is_array($value) && strpos($value, 'http:') !== false ){
|
| 910 |
//make links for urls |
| 911 |
$value = l($value, $value, array('attributes' => array('target' => '_blank')));
|
| 912 |
$value = markup_to_render_array($value); |
| 913 |
} |
| 914 |
|
| 915 |
_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value, NULL, 20); |
| 916 |
} |
| 917 |
} |
| 918 |
} |
| 919 |
} |
| 920 |
|
| 921 |
// template_preprocess_description_list() is not worting by weight so we do it right here |
| 922 |
uasort($groups, 'element_sort'); |
| 923 |
if ($isSpecimenPage) {
|
| 924 |
$sequence_elements = array( |
| 925 |
'#title' => $sequence->dnaMarker, |
| 926 |
'#theme' => 'description_list', |
| 927 |
'#groups' => $groups |
| 928 |
); |
| 929 |
} else{
|
| 930 |
$sequence_elements = array( |
| 931 |
'#title' => $sequence->dnaMarker -> titleCache, |
| 932 |
'#theme' => 'description_list', |
| 933 |
'#groups' => $groups |
| 934 |
); |
| 935 |
} |
| 936 |
|
| 937 |
return $sequence_elements; |
| 938 |
} |
| 939 |
/** |
| 940 |
* Creates an array from a list of FieldUnitDTOs. |
| 941 |
* |
| 942 |
* |
| 943 |
* @param object $specimenOrObservations |
| 944 |
* list of FieldUnitDTOs |
| 945 |
* @return array |
| 946 |
* An array containing the hierarchy of the field units corresponding to the taxon |
| 947 |
* |
| 948 |
* @ingroup compose |
| 949 |
*/ |
| 950 |
function compose_specimen_array(array $specimenOrObservations){
|
| 951 |
$items_specimen = array(); |
| 952 |
$items = array(); |
| 953 |
|
| 954 |
//we need one more item to contain the items of one level (fieldunit, derivate data etc.) |
| 955 |
foreach ($specimenOrObservations as &$specimenOrObservation) {
|
| 956 |
|
| 957 |
$items['data'] = $specimenOrObservation->listLabel ; |
| 958 |
$specimen = compose_cdm_specimen_or_observation_tree_entry($specimenOrObservation); |
| 959 |
$children = array(); |
| 960 |
$child = array(); |
| 961 |
$child['data'] =$specimen; |
| 962 |
// $children[] = create_specimen_array($specimenOrObservation->derivates); |
| 963 |
if (isset($specimenOrObservation->derivates) && sizeof($specimenOrObservation->derivates) > 0){
|
| 964 |
$child['children']= compose_specimen_array($specimenOrObservation->derivates); |
| 965 |
} |
| 966 |
$children[]=$child; |
| 967 |
$items['children'] = $children; |
| 968 |
$items_specimen[] = $items; |
| 969 |
} |
| 970 |
return $items_specimen; |
| 971 |
} |
| 972 |
|
| 973 |
|
| 974 |
/** |
| 975 |
* Compose an render array from a CDM DerivedUnitFacade object. |
| 976 |
* |
| 977 |
* compose_hook() implementation |
| 978 |
* |
| 979 |
* @param object $specimenOrObservation |
| 980 |
* the CDM instance of type SpecimenOrObservation to compose |
| 981 |
* the render array for |
| 982 |
* @param array $derivatives |
| 983 |
* the render array which contains the compositions of the derivatives |
| 984 |
* of the supplied $specimenOrObservation |
| 985 |
* |
| 986 |
* @return array |
| 987 |
* the supplied render array $derivatives to which the composition of the supplied |
| 988 |
* $specimenOrObservation has been added to |
| 989 |
* |
| 990 |
* @ingroup compose |
| 991 |
*/ |
| 992 |
|
| 993 |
function compose_cdm_specimen_or_observation_tree_entry($specimen_or_observation) |
| 994 |
{
|
| 995 |
$exclude_occurrence_fields = &drupal_static(__FUNCTION__); |
| 996 |
if (!isset($exclude_occurrence_fields)) {
|
| 997 |
$exclude_occurrence_fields = array( |
| 998 |
'type', |
| 999 |
'taxonRelatedDerivedUnits', |
| 1000 |
'label', |
| 1001 |
'titleCache', |
| 1002 |
'listLabel', |
| 1003 |
'protectedTitleCache', |
| 1004 |
'class', |
| 1005 |
'uuid', |
| 1006 |
'derivates', |
| 1007 |
'collection' |
| 1008 |
); |
| 1009 |
} |
| 1010 |
$items = array(); |
| 1011 |
|
| 1012 |
// only show uuid it the user is logged in |
| 1013 |
if (user_is_logged_in() && ($a_idx = array_search('uuid', $exclude_occurrence_fields)) !== FALSE) {
|
| 1014 |
// unset($exclude_occurrence_fields[$a_idx]); |
| 1015 |
} |
| 1016 |
|
| 1017 |
|
| 1018 |
if (is_object($specimen_or_observation)) {
|
| 1019 |
|
| 1020 |
$type_label = $specimen_or_observation->recordBase; |
| 1021 |
RenderHints::setFootnoteListKey($type_label . '-' . $specimen_or_observation->uuid); |
| 1022 |
|
| 1023 |
// collect typeStatus as label |
| 1024 |
if (isset($specimen_or_observation->specimenTypeDesignations)) {
|
| 1025 |
$type_status = array(); |
| 1026 |
foreach ($specimen_or_observation->specimenTypeDesignations as $typeDesignation) {
|
| 1027 |
if (isset($typeDesignation->typeStatus->representation_L10n)) {
|
| 1028 |
$type_status[] = $typeDesignation->typeStatus->representation_L10n; |
| 1029 |
} |
| 1030 |
} |
| 1031 |
if (count($type_status) > 0) {
|
| 1032 |
$type_label = implode(', ', $type_status);
|
| 1033 |
} |
| 1034 |
} |
| 1035 |
|
| 1036 |
$title = $type_label . ': ' . $specimen_or_observation->titleCache; |
| 1037 |
$items['data'] = $title; |
| 1038 |
|
| 1039 |
$groups = array(); |
| 1040 |
$items['children'] = $groups; |
| 1041 |
$children_items = array(); |
| 1042 |
// --- add initialized fields |
| 1043 |
foreach (get_object_vars($specimen_or_observation) as $field => $value) {
|
| 1044 |
$child_item = array(); |
| 1045 |
|
| 1046 |
if (!in_array($field, $exclude_occurrence_fields) && ($value && (!is_object($value) || isset($value->class)))) {
|
| 1047 |
switch ($field) {
|
| 1048 |
|
| 1049 |
/* ---- SpecimenOrObservationBase --- */ |
| 1050 |
case 'derivationEvent': |
| 1051 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value, NULL, 1); |
| 1052 |
break; |
| 1053 |
case 'kindOfUnit': |
| 1054 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value, NULL, 1); |
| 1055 |
break; |
| 1056 |
|
| 1057 |
|
| 1058 |
case 'preferredStableUri': |
| 1059 |
|
| 1060 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), array(array('#markup' => cdm_external_uri($value, false))));
|
| 1061 |
break; |
| 1062 |
|
| 1063 |
case 'specimenTypeDesignations': |
| 1064 |
@_description_list_group_add( |
| 1065 |
$groups, |
| 1066 |
cdm_occurrence_field_name_label($field), |
| 1067 |
array( |
| 1068 |
'#markup' => theme('cdm_typedesignations', array('typeDesignations' => $value)),
|
| 1069 |
) |
| 1070 |
); |
| 1071 |
break; |
| 1072 |
|
| 1073 |
|
| 1074 |
|
| 1075 |
case 'listOfMedia': |
| 1076 |
$gallery_settings = getGallerySettings(CDM_DATAPORTAL_SPECIMEN_GALLERY_NAME); |
| 1077 |
$captionElements = array( |
| 1078 |
'#uri' => t('open media'),
|
| 1079 |
); |
| 1080 |
$gallery_html = compose_cdm_media_gallerie(array( |
| 1081 |
'mediaList' => $value, |
| 1082 |
'galleryName' => $specimen_or_observation->label, |
| 1083 |
'maxExtend' => $gallery_settings['cdm_dataportal_media_maxextend'], |
| 1084 |
'cols' => $gallery_settings['cdm_dataportal_media_cols'], |
| 1085 |
'maxRows' => isset($gallery_settings['cdm_dataportal_media_maxRows']) ? isset($gallery_settings['cdm_dataportal_media_maxRows']) : null, |
| 1086 |
'captionElements' => $captionElements, |
| 1087 |
'mediaLinkType' => 'LIGHTBOX', |
| 1088 |
'alternativeMediaUri' => NULL, |
| 1089 |
'galleryLinkUri' => NULL, |
| 1090 |
)); |
| 1091 |
|
| 1092 |
//@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $gallery_html); |
| 1093 |
break; |
| 1094 |
|
| 1095 |
|
| 1096 |
|
| 1097 |
/* ---- DerivedUnitBase --- */ |
| 1098 |
|
| 1099 |
|
| 1100 |
case 'collectionDTO': |
| 1101 |
|
| 1102 |
$sub_dl_groups = array(); |
| 1103 |
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('code'), $value->code, NULL, 1);
|
| 1104 |
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('codeStandard'), $value->codeStandard, NULL, 2);
|
| 1105 |
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('institute'), $value->institute, NULL, 3);
|
| 1106 |
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('townOrLocation'), $value->townOrLocation, NULL, 4);
|
| 1107 |
// TODO "superCollection" |
| 1108 |
// TODO may have media |
| 1109 |
|
| 1110 |
@_description_list_group_add($groups, 'Collection', |
| 1111 |
array( |
| 1112 |
array('#markup' => $value->titleCache),
|
| 1113 |
array('#theme' => 'description_list', '#groups' => $sub_dl_groups)
|
| 1114 |
) |
| 1115 |
); |
| 1116 |
|
| 1117 |
break; |
| 1118 |
|
| 1119 |
|
| 1120 |
|
| 1121 |
|
| 1122 |
/* ---- Specimen --- */ |
| 1123 |
case 'sequences': |
| 1124 |
$dd_elements = array(); |
| 1125 |
foreach ($value as $sequence) {
|
| 1126 |
$dd_elements[] = compose_cdm_sequence($sequence, true); |
| 1127 |
$dd_elements[] = ""; |
| 1128 |
} |
| 1129 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements,'', 100); |
| 1130 |
break; |
| 1131 |
|
| 1132 |
// TODO preservation |
| 1133 |
// TODO exsiccatum |
| 1134 |
|
| 1135 |
|
| 1136 |
/* ---- FieldObservation --- */ |
| 1137 |
case 'gatheringEvent': |
| 1138 |
|
| 1139 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label('collector'), $value->collector);
|
| 1140 |
@_description_list_group_add($groups, t('Gathering date'), timePeriodToString($value->timeperiod));
|
| 1141 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label('description'), $value->description);
|
| 1142 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label('locality'), $value->locality, '', 10);
|
| 1143 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label('country'), $value->country);
|
| 1144 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label('collectingMethod'), $value->collectingMethod);
|
| 1145 |
if (isset($value->absoluteElevation)) {
|
| 1146 |
$min_max_markup = min_max_measure($value, 'absoluteElevation'); |
| 1147 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label('absoluteElevation'), $min_max_markup);
|
| 1148 |
} |
| 1149 |
if (isset($value->distanceToGround) && $value->distanceToGround >0) {
|
| 1150 |
$min_max_markup = min_max_measure($value, 'distanceToGround'); |
| 1151 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label('distanceToGround'), $min_max_markup);
|
| 1152 |
} |
| 1153 |
if (isset($value->distanceToWaterSurface) && $value->distanceToWaterSurface > 0) {
|
| 1154 |
$min_max_markup = min_max_measure($value, 'distanceToWaterSurface'); |
| 1155 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label('distanceToWaterSurface'), $min_max_markup);
|
| 1156 |
} |
| 1157 |
|
| 1158 |
if (isset($value->collectingAreas)) {
|
| 1159 |
$area_representations = array(); |
| 1160 |
foreach ($value->collectingAreas as $area) {
|
| 1161 |
// $area_representations[] = l($area->representation_L10n, path_to_named_area($area->uuid)); |
| 1162 |
$area_representations[] = $area; |
| 1163 |
} |
| 1164 |
if (!empty($area_representations)) |
| 1165 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label('collectingAreas'),
|
| 1166 |
array( |
| 1167 |
array('#markup' => implode(', ', $area_representations))
|
| 1168 |
) |
| 1169 |
); |
| 1170 |
} |
| 1171 |
if (isset($value->exactLocation) ) {
|
| 1172 |
$sub_dl_groups = array(); |
| 1173 |
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('errorRadius'), $value->exactLocation->errorRadius, ' m', 1);
|
| 1174 |
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('longitude'), round($value->exactLocation->longitude, 7), '°', 2);
|
| 1175 |
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('latitude'), round($value->exactLocation->latitude, 7), '°', 3);
|
| 1176 |
if (isset($value->exactLocation->referenceSystem)) {
|
| 1177 |
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('referenceSystem'), $value->exactLocation->referenceSystem->representation_L10n, '', 4);
|
| 1178 |
} |
| 1179 |
if ( isSet($value->exactLocation->sexagesimalString)){
|
| 1180 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label('exactLocation'),
|
| 1181 |
array( |
| 1182 |
array('#markup' => $value->exactLocation->sexagesimalString),
|
| 1183 |
array( |
| 1184 |
'#theme' => 'description_list', |
| 1185 |
'#groups' => $sub_dl_groups |
| 1186 |
), |
| 1187 |
), '', 11 |
| 1188 |
); |
| 1189 |
} |
| 1190 |
} |
| 1191 |
|
| 1192 |
break; |
| 1193 |
|
| 1194 |
/* ---- DerivationEvent --- */ |
| 1195 |
case 'derivationEvents': |
| 1196 |
//@_description_list_group_add($groups, t('Association type'), $value->description);
|
| 1197 |
break; |
| 1198 |
|
| 1199 |
|
| 1200 |
default: |
| 1201 |
if (is_object($value) || is_array($value)) {
|
| 1202 |
drupal_set_message("Unhandled type in compose_cdm_specimenOrObservation() for field " . $field, "warning");
|
| 1203 |
} else {
|
| 1204 |
_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value); |
| 1205 |
} |
| 1206 |
|
| 1207 |
} |
| 1208 |
|
| 1209 |
|
| 1210 |
} |
| 1211 |
} // END of loop over $derivedUnitFacade fields |
| 1212 |
|
| 1213 |
|
| 1214 |
|
| 1215 |
// template_preprocess_description_list() is not worting by weight so we do it right here |
| 1216 |
uasort($groups, 'element_sort'); |
| 1217 |
|
| 1218 |
$occurrence_elements = array( |
| 1219 |
// '#title' => $title, |
| 1220 |
'#theme' => 'description_list', |
| 1221 |
'#groups' => $groups, |
| 1222 |
'#attributes' => array('class' => html_class_attribute_ref($specimen_or_observation)),
|
| 1223 |
); |
| 1224 |
$output = drupal_render($occurrence_elements); |
| 1225 |
if (isset($gallery_html)){
|
| 1226 |
$output .= $gallery_html; |
| 1227 |
} |
| 1228 |
$pathToSpecimen = path_to_specimen($specimen_or_observation->uuid); |
| 1229 |
$output .= l("detail page", $pathToSpecimen, array('attributes' => array('target' => '_blank')));
|
| 1230 |
} // END of $specimenOrObservation exists |
| 1231 |
|
| 1232 |
return $output; |
| 1233 |
} |
| 1234 |
|
